title: ATTED-II provides coexpressed gene networks for Arabidopsis.
abstract: ATTED-II (http://atted.jp) is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. Here, we report updates of ATTED-II that focus especially on functionalities for constructing gene networks with regard to the following points: (i) introducing a new measure of gene coexpression to retrieve functionally related genes more accurately, (ii) implementing clickable maps for all gene networks for step-by-step navigation, (iii) applying Google Maps API to create a single map for a large network, (iv) including information about protein-protein interactions, (v) identifying conserved patterns of coexpression and (vi) showing and connecting KEGG pathway information to identify functional modules. With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis.
authors.affiliation: Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan. takeshi.obayashi@atted.jp
authors.forename: Takeshi
authors.initials: T
authors.lastname: Obayashi
authors.forename: Shinpei
authors.initials: S
authors.lastname: Hayashi
authors.forename: Motoshi
authors.initials: M
authors.lastname: Saeki
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ohta
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D025941:Protein Interaction Mapping